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comparison picard_MergeSamFiles.xml @ 8:e417b1d6288d draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
author devteam
date Tue, 06 Dec 2016 10:04:26 -0500
parents 08f69add4d06
children 486d7500da69
comparison
equal deleted inserted replaced
7:08f69add4d06 8:e417b1d6288d
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 @java_options@ 8 @java_options@
9
10 picard 9 picard
11 MergeSamFiles 10 MergeSamFiles
12 11
13 #for $element in $inputFile: 12 #for $element in $inputFile:
14 INPUT="${element}" 13 INPUT="${element}"
15 #end for 14 #end for
16 15
17 OUTPUT="${outFile}" 16 OUTPUT="${outFile}"
18 MERGE_SEQUENCE_DICTIONARIES="${merge_sequence_dictionaries}" 17 MERGE_SEQUENCE_DICTIONARIES="${merge_sequence_dictionaries}"
19 18
20 ASSUME_SORTED="${assume_sorted}" 19 ASSUME_SORTED="${assume_sorted}"
21 #for $element in $comments: 20 #for $element in $comments:
22 COMMENT="${element.comment}" 21 COMMENT="${element.comment}"
23 #end for 22 #end for
24 23
25 USE_THREADING=true 24 USE_THREADING=true
26 SORT_ORDER=coordinate 25 SORT_ORDER=coordinate
27 VALIDATION_STRINGENCY="${validation_stringency}" 26 VALIDATION_STRINGENCY="${validation_stringency}"
28 QUIET=true 27 QUIET=true
29 VERBOSITY=ERROR 28 VERBOSITY=ERROR
30 29
31 ]]></command> 30 ]]></command>
32 <inputs> 31 <inputs>
33 <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> 32 <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
34 <param name="merge_sequence_dictionaries" type="boolean" label="Merge the sequence dictionaries of the datasets being merged" help="MERGE_SEQUENCE_DICTIONARIES; default=False"/> 33 <param name="merge_sequence_dictionaries" type="boolean" label="Merge the sequence dictionaries of the datasets being merged" help="MERGE_SEQUENCE_DICTIONARIES; default=False"/>
35 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" help="ASSUME_SORTED; default=False"/> 34 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" help="ASSUME_SORTED; default=False"/>
36 35
37 <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments"> 36 <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments">
38 <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/> 37 <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/>
39 </repeat> 38 </repeat>
40 39
41 <expand macro="VS" /> 40 <expand macro="VS" />
42 41
43 </inputs> 42 </inputs>
44 43
45 <outputs> 44 <outputs>
46 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Merged BAM dataset"/> 45 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Merged BAM dataset"/>
47 </outputs> 46 </outputs>
48 47
49 <tests> 48 <tests>
50 <test> 49 <test>
51 <param name="inputFile" value="picard_MergeSamFiles_input1.bam,picard_MergeSamFiles_input2.bam,picard_MergeSamFiles_input3.bam" ftype="bam"/> 50 <param name="inputFile" value="picard_MergeSamFiles_input1.bam,picard_MergeSamFiles_input2.bam,picard_MergeSamFiles_input3.bam" ftype="bam"/>
52 <param name="assume_sorted" value="False"/> 51 <param name="assume_sorted" value="False"/>
53 <param name="merge_sequence_dictionaries" value="False"/> 52 <param name="merge_sequence_dictionaries" value="False"/>
54 <param name="validation_stringency" value="LENIENT"/> 53 <param name="validation_stringency" value="LENIENT"/>
55 <output name="outFile" file="picard_MergeSamFiles_test1.bam" ftype="bam" lines_diff="4"/> 54 <output name="outFile" file="picard_MergeSamFiles_test1.bam" ftype="bam" lines_diff="4"/>
56 </test> 55 </test>
57 </tests> 56 </tests>
58 57
59 58
60 <help> 59 <help>
61 60
62 **Purpose** 61 **Purpose**
63 62
64 Merges multiple SAM/BAM datasets into one. 63 Merges multiple SAM/BAM datasets into one.
66 @dataset_collections@ 65 @dataset_collections@
67 66
68 @description@ 67 @description@
69 68
70 ASSUME_SORTED=Boolean 69 ASSUME_SORTED=Boolean
71 AS=Boolean If true, assume that the input files are in the same sort order as the requested output 70 AS=Boolean If true, assume that the input files are in the same sort order as the requested output
72 sort order, even if their headers say otherwise. Default value: false. This option can 71 sort order, even if their headers say otherwise. Default value: false. This option can
73 be set to 'null' to clear the default value. Possible values: {true, false} 72 be set to 'null' to clear the default value. Possible values: {true, false}
74 73
75 MERGE_SEQUENCE_DICTIONARIES=Boolean 74 MERGE_SEQUENCE_DICTIONARIES=Boolean
76 MSD=Boolean Merge the sequence dictionaries Default value: false. This option can be set to 'null' 75 MSD=Boolean Merge the sequence dictionaries Default value: false. This option can be set to 'null'
77 to clear the default value. Possible values: {true, false} 76 to clear the default value. Possible values: {true, false}
78 77
79 COMMENT=String 78 COMMENT=String
80 CO=String Comment(s) to include in the merged output file's header. This option may be specified 0 79 CO=String Comment(s) to include in the merged output file's header. This option may be specified 0
81 or more times. 80 or more times.
82 81
83 82
84 @more_info@ 83 @more_info@
85 84
86 </help> 85 </help>